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Díaz CR, Hernández-Huerta MT, Mayoral LPC, Villegas MEA, Zenteno E, Cruz MM, Mayoral EPC, Del Socorro Pina Canseco M, Andrade GM, Castellanos MÁ, Matías Salvador JM, Cruz Parada E, Martínez Barras A, Cruz Fernández JN, Scott-Algara D, Pérez-Campos E. Non-Coding RNAs and Innate Immune Responses in Cancer. Biomedicines 2024; 12:2072. [PMID: 39335585 PMCID: PMC11429077 DOI: 10.3390/biomedicines12092072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/27/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Non-coding RNAs (ncRNAs) and the innate immune system are closely related, acting as defense mechanisms and regulating gene expression and innate immunity. Both are modulators in the initiation, development and progression of cancer. We aimed to review the major types of ncRNAs, including small interfering RNAs (siRNAs), microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and long non-coding RNAs (lncRNAs), with a focus on cancer, innate immunity, and inflammation. We found that ncRNAs are closely related to innate immunity, epigenetics, chronic inflammation, and cancer and share properties such as inducibility, specificity, memory, and transfer. These similarities and interrelationships suggest that ncRNAs and modulators of trained immunity, together with the control of chronic inflammation, can be combined to develop novel therapeutic approaches for personalized cancer treatment. In conclusion, the close relationship between ncRNAs, the innate immune system, and inflammation highlights their importance in cancer pathways and their potential as targets for novel therapeutic strategies.
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Affiliation(s)
| | - María Teresa Hernández-Huerta
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCyT), Facultad de Medicina y Cirugía, Universidad Autónoma "Benito Juárez" de Oaxaca (UABJO), Oaxaca 68020, Mexico
| | - Laura Pérez-Campos Mayoral
- Centro de Investigación, Facultad de Medicina UNAM-UABJO, Universidad Autónoma "Benito Juárez" de Oaxaca (UABJO), Oaxaca 68020, Mexico
| | | | - Edgar Zenteno
- Facultad de Medicina, Universidad Nacional Autónoma de Mexico, Ciudad de México 04510, Mexico
| | | | - Eduardo Pérez-Campos Mayoral
- Centro de Investigación, Facultad de Medicina UNAM-UABJO, Universidad Autónoma "Benito Juárez" de Oaxaca (UABJO), Oaxaca 68020, Mexico
| | - María Del Socorro Pina Canseco
- Centro de Investigación, Facultad de Medicina UNAM-UABJO, Universidad Autónoma "Benito Juárez" de Oaxaca (UABJO), Oaxaca 68020, Mexico
| | - Gabriel Mayoral Andrade
- Centro de Investigación, Facultad de Medicina UNAM-UABJO, Universidad Autónoma "Benito Juárez" de Oaxaca (UABJO), Oaxaca 68020, Mexico
| | | | | | - Eli Cruz Parada
- Tecnológico Nacional de México/IT Oaxaca, Oaxaca 68030, Mexico
| | | | - Jaydi Nora Cruz Fernández
- Centro de Investigación, Facultad de Medicina UNAM-UABJO, Universidad Autónoma "Benito Juárez" de Oaxaca (UABJO), Oaxaca 68020, Mexico
| | - Daniel Scott-Algara
- Unité de Biologie Cellulaire des Lymphocytes and Direction of International Affairs, Institut Pasteur, 75015 Paris, France
| | - Eduardo Pérez-Campos
- Tecnológico Nacional de México/IT Oaxaca, Oaxaca 68030, Mexico
- Laboratorio de Patología Clínica "Dr. Eduardo Pérez Ortega", Oaxaca 68000, Mexico
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Trnkova L, Buocikova V, Mego M, Cumova A, Burikova M, Bohac M, Miklikova S, Cihova M, Smolkova B. Epigenetic deregulation in breast cancer microenvironment: Implications for tumor progression and therapeutic strategies. Biomed Pharmacother 2024; 174:116559. [PMID: 38603889 DOI: 10.1016/j.biopha.2024.116559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024] Open
Abstract
Breast cancer comprises a substantial proportion of cancer diagnoses in women and is a primary cause of cancer-related mortality. While hormone-responsive cases generally have a favorable prognosis, the aggressive nature of triple-negative breast cancer presents challenges, with intrinsic resistance to established treatments being a persistent issue. The complexity intensifies with the emergence of acquired resistance, further complicating the management of breast cancer. Epigenetic changes, encompassing DNA methylation, histone and RNA modifications, and non-coding RNAs, are acknowledged as crucial contributors to the heterogeneity of breast cancer. The unique epigenetic landscape harbored by each cellular component within the tumor microenvironment (TME) adds great diversity to the intricate regulations which influence therapeutic responses. The TME, a sophisticated ecosystem of cellular and non-cellular elements interacting with tumor cells, establishes an immunosuppressive microenvironment and fuels processes such as tumor growth, angiogenesis, and extracellular matrix remodeling. These factors contribute to challenging conditions in cancer treatment by fostering a hypoxic environment, inducing metabolic stress, and creating physical barriers to drug delivery. This article delves into the complex connections between breast cancer treatment response, underlying epigenetic changes, and vital interactions within the TME. To restore sensitivity to treatment, it emphasizes the need for combination therapies considering epigenetic changes specific to individual members of the TME. Recognizing the pivotal role of epigenetics in drug resistance and comprehending the specificities of breast TME is essential for devising more effective therapeutic strategies. The development of reliable biomarkers for patient stratification will facilitate tailored and precise treatment approaches.
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Affiliation(s)
- Lenka Trnkova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Verona Buocikova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Michal Mego
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia; 2nd Department of Oncology, Comenius University, Faculty of Medicine & National Cancer Institute, Bratislava 83310, Slovakia
| | - Andrea Cumova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Monika Burikova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Martin Bohac
- 2nd Department of Oncology, Comenius University, Faculty of Medicine & National Cancer Institute, Bratislava 83310, Slovakia; Regenmed Ltd., Medena 29, Bratislava 811 01, Slovakia; Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Sasinkova 4, Bratislava 811 08, Slovakia
| | - Svetlana Miklikova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Marina Cihova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia
| | - Bozena Smolkova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 845 05, Slovakia.
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Wang Q, Zhang J, Wen Y, Qi S, Duan Y, Liu Q, Li C. The pleiotropic enhancer enh9 promotes cell proliferation and migration in non-small cell lung cancer via ERMP1 and PD-L1. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167015. [PMID: 38182069 DOI: 10.1016/j.bbadis.2023.167015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/07/2024]
Abstract
Enhancers, cis-acting DNA elements for transcriptional regulation, are important regulators of cell identity and disease. However, of the hundreds of thousands of enhancers annotated in the human genome, only a few have been studied for their regulatory mechanisms and functions in cancer progression and therapeutic resistance. Here, we report the pleiotropy of one enhancer (named enh9) in both cell proliferation and migration in non-small cell lung cancer (NSCLC) cells. By integrating multi-genomic data, ERMP1 and PD-L1 were screened out as potential targets of enh9. CUT&Tag sequencing demonstrated that enh9 was involved in the genomic interactions between the transcription factor RELA and the promoters of ERMP1 and PD-L1. In addition, ERMP1 and PD-L1 were validated to be involved in cell proliferation and migration, respectively. Our study fully elucidated the function and transcriptional regulation mechanisms of enh9 in NSCLC. The exploration on enhancers is promising to provide new insights for cancer diagnosis and therapy.
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Affiliation(s)
- Qilin Wang
- School of Engineering Medicine, Beihang University, Beijing 100191, China; Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China; School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Junyou Zhang
- School of Engineering Medicine, Beihang University, Beijing 100191, China; Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China; School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yanling Wen
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, Guangdong 518112, China; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Sihan Qi
- School of Engineering Medicine, Beihang University, Beijing 100191, China; Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China; School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yingying Duan
- School of Engineering Medicine, Beihang University, Beijing 100191, China; Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China; School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Qian Liu
- School of Engineering Medicine, Beihang University, Beijing 100191, China; Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China; School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Chunyan Li
- School of Engineering Medicine, Beihang University, Beijing 100191, China; Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China; School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing 100191, China.
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Zhang C, Liang S, Zhang H, Wang R, Qiao H. Epigenetic regulation of mRNA mediates the phenotypic plasticity of cancer cells during metastasis and therapeutic resistance (Review). Oncol Rep 2024; 51:28. [PMID: 38131215 PMCID: PMC10777459 DOI: 10.3892/or.2023.8687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Plasticity, the ability of cancer cells to transition between differentiation states without genomic alterations, has been recognized as a major source of intratumoral heterogeneity. It has a crucial role in cancer metastasis and treatment resistance. Thus, targeting plasticity holds tremendous promise. However, the molecular mechanisms of plasticity in cancer cells remain poorly understood. Several studies found that mRNA, which acts as a bridge linking the genetic information of DNA and protein, has an important role in translating genotypes into phenotypes. The present review provided an overview of the regulation of cancer cell plasticity occurring via changes in the transcription and editing of mRNAs. The role of the transcriptional regulation of mRNA in cancer cell plasticity was discussed, including DNA‑binding transcriptional factors, DNA methylation, histone modifications and enhancers. Furthermore, the role of mRNA editing in cancer cell plasticity was debated, including mRNA splicing and mRNA modification. In addition, the role of non‑coding (nc)RNAs in cancer plasticity was expounded, including microRNAs, long intergenic ncRNAs and circular RNAs. Finally, different strategies for targeting cancer cell plasticity to overcome metastasis and therapeutic resistance in cancer were discussed.
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Affiliation(s)
- Chunzhi Zhang
- Department of Radiation Oncology, Tianjin Hospital, Tianjin University, Tianjin 300211, P.R. China
| | - Siyuan Liang
- Functional Materials Laboratory, Institute of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300211, P.R. China
| | - Hanning Zhang
- Clinical Medical College of Tianjin Medical University, Tianjin 300270, P.R. China
| | - Ruoxi Wang
- Sophomore, Farragut School #3 of Yangtai Road, Tianjin 300042, P.R. China
| | - Huanhuan Qiao
- Functional Materials Laboratory, Institute of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300211, P.R. China
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Lewis MW, Wisniewska K, King CM, Li S, Coffey A, Kelly MR, Regner MJ, Franco HL. Enhancer RNA Transcription Is Essential for a Novel CSF1 Enhancer in Triple-Negative Breast Cancer. Cancers (Basel) 2022; 14:1852. [PMID: 35406623 PMCID: PMC8997997 DOI: 10.3390/cancers14071852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/24/2022] [Accepted: 03/29/2022] [Indexed: 12/11/2022] Open
Abstract
Enhancers are critical regulatory elements in the genome that help orchestrate spatiotemporal patterns of gene expression during development and normal physiology. In cancer, enhancers are often rewired by various genetic and epigenetic mechanisms for the activation of oncogenes that lead to initiation and progression. A key feature of active enhancers is the production of non-coding RNA molecules called enhancer RNAs, whose functions remain unknown but can be used to specify active enhancers de novo. Using a combination of eRNA transcription and chromatin modifications, we have identified a novel enhancer located 30 kb upstream of Colony Stimulating Factor 1 (CSF1). Notably, CSF1 is implicated in the progression of breast cancer, is overexpressed in triple-negative breast cancer (TNBC) cell lines, and its enhancer is primarily active in TNBC patient tumors. Genomic deletion of the enhancer (via CRISPR/Cas9) enabled us to validate this regulatory element as a bona fide enhancer of CSF1 and subsequent cell-based assays revealed profound effects on cancer cell proliferation, colony formation, and migration. Epigenetic silencing of the enhancer via CRISPR-interference assays (dCas9-KRAB) coupled to RNA-sequencing, enabled unbiased identification of additional target genes, such as RSAD2, that are predictive of clinical outcome. Additionally, we repurposed the RNA-guided RNA-targeting CRISPR-Cas13 machinery to specifically degrade the eRNAs transcripts produced at this enhancer to determine the consequences on CSF1 mRNA expression, suggesting a post-transcriptional role for these non-coding transcripts. Finally, we test our eRNA-dependent model of CSF1 enhancer function and demonstrate that our results are extensible to other forms of cancer. Collectively, this work describes a novel enhancer that is active in the TNBC subtype, which is associated with cellular growth, and requires eRNA transcripts for proper enhancer function. These results demonstrate the significant impact of enhancers in cancer biology and highlight their potential as tractable targets for therapeutic intervention.
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Affiliation(s)
- Michael W. Lewis
- The Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (M.W.L.); (K.W.); (C.M.K.); (S.L.); (A.C.); (M.R.K.); (M.J.R.)
| | - Kamila Wisniewska
- The Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (M.W.L.); (K.W.); (C.M.K.); (S.L.); (A.C.); (M.R.K.); (M.J.R.)
| | - Caitlin M. King
- The Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (M.W.L.); (K.W.); (C.M.K.); (S.L.); (A.C.); (M.R.K.); (M.J.R.)
| | - Shen Li
- The Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (M.W.L.); (K.W.); (C.M.K.); (S.L.); (A.C.); (M.R.K.); (M.J.R.)
| | - Alisha Coffey
- The Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (M.W.L.); (K.W.); (C.M.K.); (S.L.); (A.C.); (M.R.K.); (M.J.R.)
| | - Michael R. Kelly
- The Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (M.W.L.); (K.W.); (C.M.K.); (S.L.); (A.C.); (M.R.K.); (M.J.R.)
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew J. Regner
- The Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (M.W.L.); (K.W.); (C.M.K.); (S.L.); (A.C.); (M.R.K.); (M.J.R.)
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hector L. Franco
- The Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (M.W.L.); (K.W.); (C.M.K.); (S.L.); (A.C.); (M.R.K.); (M.J.R.)
- Bioinformatics and Computational Biology Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- The Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Ruzic D, Djoković N, Srdić-Rajić T, Echeverria C, Nikolic K, Santibanez JF. Targeting Histone Deacetylases: Opportunities for Cancer Treatment and Chemoprevention. Pharmaceutics 2022; 14:pharmaceutics14010209. [PMID: 35057104 PMCID: PMC8778744 DOI: 10.3390/pharmaceutics14010209] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
The dysregulation of gene expression is a critical event involved in all steps of tumorigenesis. Aberrant histone and non-histone acetylation modifications of gene expression due to the abnormal activation of histone deacetylases (HDAC) have been reported in hematologic and solid types of cancer. In this sense, the cancer-associated epigenetic alterations are promising targets for anticancer therapy and chemoprevention. HDAC inhibitors (HDACi) induce histone hyperacetylation within target proteins, altering cell cycle and proliferation, cell differentiation, and the regulation of cell death programs. Over the last three decades, an increasing number of synthetic and naturally derived compounds, such as dietary-derived products, have been demonstrated to act as HDACi and have provided biological and molecular insights with regard to the role of HDAC in cancer. The first part of this review is focused on the biological roles of the Zinc-dependent HDAC family in malignant diseases. Accordingly, the small-molecules and natural products such as HDACi are described in terms of cancer therapy and chemoprevention. Furthermore, structural considerations are included to improve the HDACi selectivity and combinatory potential with other specific targeting agents in bifunctional inhibitors and proteolysis targeting chimeras. Additionally, clinical trials that combine HDACi with current therapies are discussed, which may open new avenues in terms of the feasibility of HDACi’s future clinical applications in precision cancer therapies.
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Affiliation(s)
- Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Nemanja Djoković
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Tatjana Srdić-Rajić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
| | - Cesar Echeverria
- Facultad de Medicina, Universidad de Atacama, Copayapu 485, Copiapo 1531772, Chile;
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (D.R.); (N.D.); (K.N.)
| | - Juan F. Santibanez
- Group for Molecular Oncology, Institute for Medical Research, National Institute of the Republic of Serbia, University of Belgrade, Dr. Subotica 4, POB 102, 11129 Belgrade, Serbia
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago 8370854, Chile
- Correspondence: ; Tel.: +381-11-2685-788; Fax: +381-11-2643-691
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